- Mozilla Firefox (but only when I encounter a page Safari can't handle which is almost never)
- remind - Explanation of why
- vim and gvim
- iTerm
- VoodooPad (free for non commercial)
- Perl (it's technically an open source app when you think about it)
- Ruby (see perl)
- Quicksilver - if you own an OS X machine and don't have this, you're missing out on how all computers should work. Learn Why even Windows users should check this app out just so they can tell Windows developers what they should be making.
- BitTorrent
- Adium
- ClamAV and OS X interface
- SubEthaEdit (free for non commercial and another example of how apps should be made on all platforms)
- Plucker
- HandyShopper on the Palm
- FileZ on the Palm
- NetHack on every computer I own (my sad addiction)
There's got to be more. I never buy an application until after I've at least tried to find a free alternative so I'm sure there's tons more on here (I know I use a ton of freeware for little utility things like running system maintenance scripts at pre-determined intervals or printing PDFs in a booklet format (which is the same as printing to a booklet format from any program in OS X

)). That's just the list of things I could think of off the top of my head, things I use a lot or are important for some reason (except FireFox which I really don't use much at all).
I'm not even thinking about all the server software I've used over the years like Apache and MySQL and whatnot. Honestly, I marvel at administrators who pay for server software and get inferior products most of the time (databases can be the exception to that rule, a good RDBMS is still worth a lot of money if you really need it (most people don't need it though and MySQL or PostGRESQL are fine)). For just about everything else you'd put on a server, the freeware options are superior to most purchased ones. Easier to admin (for an admin who understands what the server is doing, and every good admin should) too which just makes the continued use of MS software baffling to me.